Wikiomics:Protein mass spectrometry - Revision history

Darek Kedra: /* Protein databases */ uShuffle+

Darek Kedra — Fri, 01 Aug 2008 15:14:43 GMT

Protein databases: uShuffle+

←Older revision		Revision as of 15:14, 1 August 2008
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	*** MEGGAYGAGKAGGAFDPYTL => FYAGADEAGMGTYKGGAGLP (used [http://host9.bioinfo3.ifom-ieo-campus.it/sms2/shuffle_protein.html SMS], results differ each time) -> recommended by EBI ppl		*** MEGGAYGAGKAGGAFDPYTL => FYAGADEAGMGTYKGGAGLP (used [http://host9.bioinfo3.ifom-ieo-campus.it/sms2/shuffle_protein.html SMS], results differ each time) -> recommended by EBI ppl
	** random (i.e. creating database of random proteins based on frequency of AA in source fasta file)		** random (i.e. creating database of random proteins based on frequency of AA in source fasta file)
		+
	* to create decoy database use [http://genesis.ugent.be/dbtoolkit/ DBToolkit] free java standalone		* to create decoy database use [http://genesis.ugent.be/dbtoolkit/ DBToolkit] free java standalone
		+	* experimental: [http://www.cs.usu.edu/~mjiang/ushuffle/ uShuffle] "generating uniform random permutations of biological sequencest hat preserve the exact k-let counts" i.e dipeptides

	===Modification databases===		===Modification databases===

James Atwood: /* $$$ programs */

James Atwood — Sat, 21 Jun 2008 16:56:22 GMT

$$$ programs

←Older revision		Revision as of 16:56, 21 June 2008
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	== $$$ programs ==		== $$$ programs ==
	* [http://www.waters.com/WatersDivision/contentd.asp?watersit=RHEY-5LHBSW ProteinLynx Global SERVER] $$$, from Waters Waters Corporation		* [http://www.waters.com/WatersDivision/contentd.asp?watersit=RHEY-5LHBSW ProteinLynx Global SERVER] $$$, from Waters Waters Corporation
-	* [http://phenyx.vital-it.ch/pwi/ Phenyx] from GeneBio (online web server)	+	* [http://phenyx.vital-it.ch/pwi/ Phenyx] from GeneBio (online web server)
		+	* [http://www.bioinquire.com ProteoIQ] from BIOINQUIRE

	==Other==		==Other==

Torsten Waldminghaus: added tags

Torsten Waldminghaus — Mon, 03 Mar 2008 20:57:30 GMT

added tags

←Older revision		Revision as of 20:57, 3 March 2008
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	* [[User:Darked\|Darek Kedra]] wrote this tutorial		* [[User:Darked\|Darek Kedra]] wrote this tutorial
	<!-- other contributors, put yourself here -->		<!-- other contributors, put yourself here -->
		+
		+
		+	[[Category:Protocol]]
		+	[[Category:In silico]]
		+	[[Category:Data analysis]]

Darek Kedra: /* Biblio */

Darek Kedra — Thu, 17 Jan 2008 19:57:20 GMT

Biblio

←Older revision		Revision as of 19:57, 17 January 2008
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	{{stub}}-->		{{stub}}-->
		+
		+	=Biblio=
		+
		+	#Brun, Virginie, Alain Dupuis, Annie Adrait, Marlene Marcellin, Damien Thomas, Magali Court, et al. “Isotope-labeled Protein Standards: Toward Absolute Quantitative Proteomics.” Mol Cell Proteomics 6, no. 12 (December 1, 2007): 2139-2149.
		+	#Carr, Steven, Ruedi Aebersold, Michael Baldwin, Al Burlingame, Karl Clauser, and Alexey Nesvizhskii. “The Need for Guidelines in Publication of Peptide and Protein Identification Data: Working Group On Publication Guidelines For Peptide And Protein Identification Data.” Mol Cell Proteomics 3, no. 6 (June 1, 2004): 531-533.
		+	#Craig, Robertson, and Ronald C. Beavis. “TANDEM: matching proteins with tandem mass spectra.” Bioinformatics 20, no. 9 (June 12, 2004): 1466-1467.
		+	#Domon, Bruno, and Ruedi Aebersold. “Mass Spectrometry and Protein Analysis.” Science 312, no. 5771 (April 14, 2006): 212-217.
		+	#Elias, Joshua E, and Steven P Gygi. “Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry.” Nat Meth 4, no. 3 (March 2007): 207-214.
		+	#Elias, Joshua E, Wilhelm Haas, Brendan K Faherty, and Steven P Gygi. “Comparative evaluation of mass spectrometry platforms used in large-scale proteomics investigations.” Nat Meth 2, no. 9 (2005): 667-675.
		+	#Eng, Jimmy K., Ashley L. McCormack, and John R. Yates. “An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database.” Journal of the American Society for Mass Spectrometry 5, no. 11 (November 1994): 976-989.
		+	#Kersey, Paul J., Jorge Duarte, Allyson Williams, Youla Karavidopoulou, Ewan Birney, and Rolf Apweiler. “The International Protein Index: An integrated database for proteomics experiments.” PROTEOMICS 4, no. 7 (2004): 1985-1988.
		+	#Kim, Sangtae, Seungjin Na, Ji Woong Sim, Heejin Park, Jaeho Jeong, Hokeun Kim, et al. “MODi : a powerful and convenient web server for identifying multiple post-translational peptide modifications from tandem mass spectra.” Nucl. Acids Res. 34, no. suppl_2 (July 1, 2006): W258-263.
		+	#Martens, Lennart, Sandra Orchard, Rolf Apweiler, and Henning Hermjakob. “Human Proteome Organization Proteomics Standards Initiative: Data Standardization, a View on Developments and Policy.” Mol Cell Proteomics 6, no. 9 (September 1, 2007): 1666-1667.
		+	#Perkins, David N., Darryl J. C. Pappin, David M. Creasy, and John S. Cottrell. “Probability-based protein identification by searching sequence databases using mass spectrometry data.” Electrophoresis 20, no. 18 (1999): 3551-3567.
		+	#Roos, Franz F., Riko Jacob, Jonas Grossmann, Bernd Fischer, Joachim M. Buhmann, Wilhelm Gruissem, et al. “PepSplice: cache-efficient search algorithms for comprehensive identification of tandem mass spectra.” Bioinformatics 23, no. 22 (November 15, 2007): 3016-3023.
		+	#Webb-Robertson, Bobbie-Jo M., and William R. Cannon. “Current trends in computational inference from mass spectrometry-based proteomics.” Brief Bioinform 8, no. 5 (September 1, 2007): 304-317.
		+

	=Credits=		=Credits=

Leptos at 15:43, 15 December 2007

Leptos — Sat, 15 Dec 2007 15:43:58 GMT

←Older revision		Revision as of 15:43, 15 December 2007
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	* software		* software
-	** [http://tools.proteomecenter.org/wiki/index.php?title=Software:ASAPRatio ASAPRatio] from Trans Proteomics Pipeline:	+	** [http://tools.proteomecenter.org/wiki/index.php?title=Software:ASAPRatio ASAPRatio] from Trans Proteomics Pipeline:<br>"calculates the relative abundances of proteins and the corresponding confidence intervals from ICAT-type ESI-LC/MS data"
-	"calculates the relative abundances of proteins and the corresponding confidence intervals from ICAT-type ESI-LC/MS data"	+
	** [http://msquant.sourceforge.net/ MSQuant] Parser for Mascot results for quantitation (Windows only)		** [http://msquant.sourceforge.net/ MSQuant] Parser for Mascot results for quantitation (Windows only)
-		+	** [http://arep.med.harvard.edu/mapquant-suite.html MapQuant Suite]
	=Frameworks/pipelines=		=Frameworks/pipelines=
	* [http://tools.proteomecenter.org/TPP.php Trans Proteomic Pipeline ] (TPP) most popular, included in Sorcerer from Sage-N Research. Windows/Cygwin/Perl or Linux based.		* [http://tools.proteomecenter.org/TPP.php Trans Proteomic Pipeline ] (TPP) most popular, included in Sorcerer from Sage-N Research. Windows/Cygwin/Perl or Linux based.

Darek Kedra: /* de novo sequence determination algorithms */

Darek Kedra — Fri, 14 Dec 2007 21:19:26 GMT

de novo sequence determination algorithms

←Older revision		Revision as of 21:19, 14 December 2007
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	==de novo sequence determination algorithms==		==de novo sequence determination algorithms==
-	* PepNovo: [http://~~darwin~~.~~informatics~~.~~indiana.edu~~/~~col~~/~~meeting~~/~~2005_10~~/~~PepNovo.pdf (PDF)]~~	+	For comparison see: Performance Evaluation of Existing De Novo Sequencing Algorithms by Pevtsov et al. (2006) [http://pubs.acs.org/cgi-bin/article.cgi/jprobs/2006/5/i11/pdf/pr060222h.pdf PDF]
-	* Sherenga [http://~~www.liebertonline.com~~/~~doi~~/~~pdfplus/10~~.~~1089/106652799318300 (~~PDF)]	+	===Comonly used===
	* Peaks [http://www.bioinformatics.uwaterloo.ca/papers/03peaks.pdf (PDF)]		* Peaks [http://www.bioinformatics.uwaterloo.ca/papers/03peaks.pdf (PDF)]
		+	* PepNovo: [http://darwin.informatics.indiana.edu/col/meeting/2005_10/PepNovo.pdf (PDF)]
	* Lutefisk [http://www.hairyfatguy.com/Lutefisk/ web]		* Lutefisk [http://www.hairyfatguy.com/Lutefisk/ web]
		+	* Sherenga [http://www.liebertonline.com/doi/pdfplus/10.1089/106652799318300 (PDF)]
		+
		+	===Novel===
		+	These (according to authors) are better than any of the four listed above
		+	* [http://people.inf.ethz.ch/befische/proteomics/ NovoHMM] for non-commercial use only, Windows binary. Model file for ThermoFinnigan LCQ mass spectrometer.
		+	According to Pevtsov NovoHMM has the best sensitivity, and its performance is the best in the entire range of spectrum quality. But the overall performance of NovoHMM is not significantly different from the performance of PEAKS and PepNovo.
		+
		+	* NovoHMM++

	==Spectral matching ==		==Spectral matching ==

Darek Kedra: +test data sets, tutorial

Darek Kedra — Tue, 11 Dec 2007 18:41:45 GMT

+test data sets, tutorial

←Older revision		Revision as of 18:41, 11 December 2007
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	* quantification		* quantification

		+	A good introductory tutorial from USC Computational Biology group is [http://msms.cmb.usc.edu/tutorial.html here].

	=Protein/peptide identification=		=Protein/peptide identification=
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	* algorithms (most commonly used):		* algorithms (most commonly used):
	** [http://fields.scripps.edu/sequest/index.html Sequest] $$$		** [http://fields.scripps.edu/sequest/index.html Sequest] $$$
-	** [http://www.matrixscience.com/home.html Mascot] $$$	+	** [http://www.matrixscience.com/home.html Mascot] $$$, free but limited [http://www.matrixscience.com/cgi/search_form.pl?FORMVER=2&SEARCH=MIS web server form]
	** [http://pubchem.ncbi.nlm.nih.gov/omssa/ OMSSA] Open Mass Spectrometry Search Algorithm, open source		** [http://pubchem.ncbi.nlm.nih.gov/omssa/ OMSSA] Open Mass Spectrometry Search Algorithm, open source
	** [http://thegpm.org/ XTandem] open source effort from Canada		** [http://thegpm.org/ XTandem] open source effort from Canada
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	* [http://p3.thegpm.org/tandem/ppp.html P3 (server)] from Global Proteomics Machine (free)		* [http://p3.thegpm.org/tandem/ppp.html P3 (server)] from Global Proteomics Machine (free)
	** [http://www.thegpm.org/PPP/index.html description]		** [http://www.thegpm.org/PPP/index.html description]
-	* [http://www.peptideatlas.org/spectrast/ SpectraST] from ISB, Seattle (not as many species/options as P3)	+	* [http://www.peptideatlas.org/spectrast/ SpectraST] from ISB, Seattle (not as many species/options as P3). Ca 500x faster than Sequest on the same set.
		+	[http://www.proteomecenter.org/course/spectraST.11.07.pdf lecture notes] by Henry Lam from ISB
		+
	* [http://proteome.gs.washington.edu/software/bibliospec/documentation/index.html BiblioSpec] from MacCoss lab. (free for non-profit, online licence)		* [http://proteome.gs.washington.edu/software/bibliospec/documentation/index.html BiblioSpec] from MacCoss lab. (free for non-profit, online licence)
	** command line only		** command line only
		+
		+	Spectral libraries available [http://www.peptideatlas.org/speclib/ here@PeptideAtlas]

	=Protein quantification=		=Protein quantification=
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	* '''mzData''' (standard set by HUPO Proteomics Standard Initiative)		* '''mzData''' (standard set by HUPO Proteomics Standard Initiative)

		+	=Spectrum datasets=
		+	Good for testing programs:
		+	* [http://www.peptideatlas.org/ PeptideAtlas@ Seattle Proteome Center]
		+
		+	* Open Proteomics Database [http://bioinformatics.icmb.utexas.edu/OPD/ OPD]
		+	* [http://www.ebi.ac.uk/pride/ppp_links.do HUPO Plasma Proteome Project files] PRIDE@EBI

	=Web sites=		=Web sites=
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	* [http://www.proteomecommons.org/tools.jsp Proteome Commons] collection of tools & links		* [http://www.proteomecommons.org/tools.jsp Proteome Commons] collection of tools & links
	* [http://www.broad.mit.edu/cancer/software/genepattern/desc/proteomics.html GenePattern] proteomics modules from Broad Inst.		* [http://www.broad.mit.edu/cancer/software/genepattern/desc/proteomics.html GenePattern] proteomics modules from Broad Inst.
-		+	* [http://msms.cmb.usc.edu/ USC in LA] several programs: PepHMM, Sub-DeNovo, SuffixTree-MS.
	=Reviews=		=Reviews=
	For a good review of programs and aspects of protein identification by mass spectrometry		For a good review of programs and aspects of protein identification by mass spectrometry
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	==Other==		==Other==
		+	Needs to be sorted out.
		+
	* [http://www.bioinfo.no/software/massSorter massSorter ]		* [http://www.bioinfo.no/software/massSorter massSorter ]
	* [http://prospector.ucsf.edu/ ProteinProspector]		* [http://prospector.ucsf.edu/ ProteinProspector]
		+	===Experimental===
	* [http://bioinformatics.genomicsolutions.com/service/prowl/sonar.html Sonar ]		* [http://bioinformatics.genomicsolutions.com/service/prowl/sonar.html Sonar ]

	* DeNovoID [http://proteomics.mcw.edu/denovoid web]		* DeNovoID [http://proteomics.mcw.edu/denovoid web]
-	* SPIDER [http://ieeexplore.ieee.org/iel5/9262/29416/01332434.pdf?tp=&isnumber=&arnumber=1332434 (PDF)] de novo + homology search in other species	+	* SPIDER [http://ieeexplore.ieee.org/iel5/9262/29416/01332434.pdf?tp=&isnumber=&arnumber=1332434 (PDF)] de novo + homology search in other species based on a set of tags
	* OpenSea [http://pubs.acs.org/cgi-bin/article.cgi/jprobs/2005/4/i02/html/pr049781j.html (HTML)] Java program available from authors		* OpenSea [http://pubs.acs.org/cgi-bin/article.cgi/jprobs/2005/4/i02/html/pr049781j.html (HTML)] Java program available from authors
-
-	* ModifiComb [http://www.mcponline.org/cgi/content/full/5/5/935 (HTML)] (available from authors?)
-	* [http://prix.uos.ac.kr/modi/ MODi] web server for PTMs discovery

		+	ModifiComb [http://www.mcponline.org/cgi/content/full/5/5/935 (HTML)] (available from authors?)
		+	* [http://prix.uos.ac.kr/modi/ MODi] web server for PTMs discovery
	* [http://llama.med.harvard.edu/cgi/SILVER/silver.cgi?id=916487 SILVER] view your spectra with LOD scores		* [http://llama.med.harvard.edu/cgi/SILVER/silver.cgi?id=916487 SILVER] view your spectra with LOD scores
		+
		+

	<!--		<!--

Darek Kedra: /* File formats */

Darek Kedra — Thu, 29 Nov 2007 13:10:43 GMT

File formats

←Older revision		Revision as of 13:10, 29 November 2007
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	* [http://www.sagenresearch.com/products.html Sorcerer] $$$ FPGA-based fast hardware solution for SEQUEST & Tandem searches with TPP on top of it.		* [http://www.sagenresearch.com/products.html Sorcerer] $$$ FPGA-based fast hardware solution for SEQUEST & Tandem searches with TPP on top of it.

		+	=File formats=
		+	* '''.bdx''' from Bruker Daltonics
		+	* '''.dta''' SEQUEST/Thermoelectron. Two versions:
		+	** single pectra
		+	** multiple spectra concateneted in one file
		+	* '''.mgf''' multiple spectra, Mascot (Matrix science)
		+	* '''mzXML''' (used by Trans Proteomics Pipeline)
		+	* '''mzData''' (standard set by HUPO Proteomics Standard Initiative)
		+
		+
	=Web sites=		=Web sites=
	* [http://peptide.ucsd.edu/Software.html UCSD (Pevzner)]		* [http://peptide.ucsd.edu/Software.html UCSD (Pevzner)]

Darek Kedra: /* Protein quantification */

Darek Kedra — Mon, 26 Nov 2007 16:12:36 GMT

Protein quantification

←Older revision		Revision as of 16:12, 26 November 2007
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	** isotopic labeling (ICAT, ITRAQ, SILAC, 18O- or 15N-labeling)		** isotopic labeling (ICAT, ITRAQ, SILAC, 18O- or 15N-labeling)
	**label-free methods		**label-free methods
		+	** [http://www.proteomics.be/proteomics/cofradic/index.html COFRADIC]

	* software		* software

Darek Kedra: /* Other tools to be sorted out */

Darek Kedra — Mon, 26 Nov 2007 15:38:04 GMT

Other tools to be sorted out

←Older revision		Revision as of 15:38, 26 November 2007
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	* [http://dove.embl-heidelberg.de/Blast2/msblast.html MS-BLAST]		* [http://dove.embl-heidelberg.de/Blast2/msblast.html MS-BLAST]

-	== $$$ programs ===	+	== $$$ programs ==
	* [http://www.waters.com/WatersDivision/contentd.asp?watersit=RHEY-5LHBSW ProteinLynx Global SERVER] $$$, from Waters Waters Corporation		* [http://www.waters.com/WatersDivision/contentd.asp?watersit=RHEY-5LHBSW ProteinLynx Global SERVER] $$$, from Waters Waters Corporation
	* [http://phenyx.vital-it.ch/pwi/ Phenyx] from GeneBio (online web server)		* [http://phenyx.vital-it.ch/pwi/ Phenyx] from GeneBio (online web server)